Gaia Andreoletti
YOU?
Author Swipe
View article: Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research
Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research Open
View article: Critical assessment of missense variant effect predictors on disease-relevant variant data
Critical assessment of missense variant effect predictors on disease-relevant variant data Open
Regular, systematic, and independent assessments of computational tools that are used to predict the pathogenicity of missense variants are necessary to evaluate their clinical and research utility and guide future improvements. The Critic…
View article: A differentiated β-globin gene replacement strategy uses heterologous introns to restore physiological expression
A differentiated β-globin gene replacement strategy uses heterologous introns to restore physiological expression Open
View article: VMAP: Vaginal Microbiome Atlas during Pregnancy
VMAP: Vaginal Microbiome Atlas during Pregnancy Open
Objectives To enable interactive visualization of the vaginal microbiome across the pregnancy and facilitate discovery of novel insights and generation of new hypotheses. Material and Methods Vaginal Microbiome Atlas during Pregnancy (VMAP…
View article: Critical assessment of missense variant effect predictors on disease-relevant variant data
Critical assessment of missense variant effect predictors on disease-relevant variant data Open
Regular, systematic, and independent assessment of computational tools used to predict the pathogenicity of missense variants is necessary to evaluate their clinical and research utility and suggest directions for future improvement. Here,…
View article: Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair
Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair Open
View article: CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods Open
View article: Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research
Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research Open
View article: A benchmark for large language models in bioinformatics
A benchmark for large language models in bioinformatics Open
The rapid advancements in artificial intelligence, particularly in Large Language Models (LLMs) such as GPT-4, Gemini, and LLaMA, have opened new avenues for computational biology and bioinformatics. We report the development of BioLLMBenc…
View article: AI Competitions and Benchmarks: The life cycle of challenges and benchmarks
AI Competitions and Benchmarks: The life cycle of challenges and benchmarks Open
Data Science research is undergoing a revolution fueled by the transformative power of technology, the Internet, and an ever increasing computational capacity. The rate at which sophisticated algorithms can be developed is unprecedented, y…
View article: Functional Screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair
Functional Screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair Open
Homology Directed Repair (HDR) enables precise genome editing and holds great promise in the gene therapy field. However, the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alt…
View article: High-throughput transcriptome analyses from ASPIRO, a phase 1/2/3 study of gene replacement therapy for X-linked myotubular myopathy
High-throughput transcriptome analyses from ASPIRO, a phase 1/2/3 study of gene replacement therapy for X-linked myotubular myopathy Open
View article: Loss of Mtm1 causes cholestatic liver disease in a model of X-linked myotubular myopathy
Loss of Mtm1 causes cholestatic liver disease in a model of X-linked myotubular myopathy Open
X-linked myotubular myopathy (XLMTM) is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently, there are no approved treatments, although AAV8-mediated gene transfer therapy has shown promise in animal models and prel…
View article: VMAP: Vaginal Microbiome Atlas During Pregnancy
VMAP: Vaginal Microbiome Atlas During Pregnancy Open
The vaginal microbiome has been shown to be associated with pregnancy outcomes including preterm birth (PTB) risk. Here we present VMAP: Vaginal Microbiome Atlas during Pregnancy ( http://vmapapp.org ), an application to visualize features…
View article: Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research
Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research Open
Globally, every year about 11% of infants are born preterm, defined as a birth prior to 37 weeks of gestation, with significant and lingering health consequences. Multiple studies have related the vaginal microbiome to preterm birth. We pr…
View article: Identifying Age-Specific Transcriptomic and Metabolomic Changes Induced by <i>apoE</i> Genotype in Mice
Identifying Age-Specific Transcriptomic and Metabolomic Changes Induced by <i>apoE</i> Genotype in Mice Open
View article: A transcriptional switch governs fibroblast activation in heart disease
A transcriptional switch governs fibroblast activation in heart disease Open
View article: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 Open
The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We uti…
View article: Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth Open
Identification of pregnancies at risk of preterm birth (PTB), the leading cause of newborn deaths, remains challenging given the syndromic nature of the disease. We report a longitudinal multi-omics study coupled with a DREAM challenge to …
View article: Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures
Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures Open
Systemic lupus erythematosus (SLE) is an autoimmune disease in which outcomes vary among different racial groups. We leverage cell-sorted RNA-seq data (CD14+ monocytes, B cells, CD4+ T cells, and NK cells) from 120 SLE patients (63 Asian a…
View article: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 Open
The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We uti…
View article: metaData
metaData Open
metaData
View article: metaData
metaData Open
metaData
View article: metaData
metaData Open
metaData
View article: Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity Open
View article: Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus
Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus Open
Systemic lupus erythematosus (SLE) is an autoimmune disease in which outcomes vary among different racial groups. We leverage cell-sorted RNA-seq data (CD14 + monocytes, B cells, CD4 + T cells, and NK cells) from 120 SLE patients (63 Asian…
View article: Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus
Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus Open
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease in which outcomes vary among different racial groups. The aim of this study is to leverage large-scale transcriptomic data from diverse populations to better sub-clas…
View article: BRD4 (Bromodomain-Containing Protein 4) Interacts with GATA4 (GATA Binding Protein 4) to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes
BRD4 (Bromodomain-Containing Protein 4) Interacts with GATA4 (GATA Binding Protein 4) to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes Open
Background: Gene regulatory networks control tissue homeostasis and disease progression in a cell type–specific manner. Ubiquitously expressed chromatin regulators modulate these networks, yet the mechanisms governing how tissue specificit…
View article: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 Open
The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We uti…
View article: A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease
A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease Open
In diseased organs, stress-activated signaling cascades alter chromatin, triggering broad shifts in transcription and cell state that exacerbate pathology. Fibroblast activation is a common stress response that worsens lung, liver, kidney …